Pawel Swietach - Novel insights into tumour acidosis and hypoxia from analyses of mutations, phenotypes and blood oxygen transport

The project relates to two pillars of research activity in the Swietach group: in relation to cancer and in relation to blood. The connecting theme is hypoxia and acidosis, which is a chemical signature of the tumour microenvironment, and is shaped by the properties of red cells that carry oxygen and handle acid. The work will be primarily “dry lab” but with an element of “wet lab” testing of key predictions and hypotheses. The successful candidate will be proficient in handling large data from public repositories as well as curating in-house data, and will have an appropriate level of skills to perform statistical analyses. It is desirable that the candidate has strengths in mathematics to generate simulations. The main programming environments will be R and MATLAB, with training available.  

The work will be divided into three components that may run concurrently. 

1. Using mutational data on human cancers to understand the role of ion transporters relevant to pH regulation. We have used TCGA databases to show that certain tumors accumulate an above-background number of mutations in ion transporters of the SLC family that are relevant to pH control. An example of such a tumor is endometrial cancer, ostensibly because of its hypoxic environment. The gene SLC4A3 is relatively frequently mutated, but the functional significance of this in terms of tumour acidosis is unclear. Loss or gain of function mutations in this and related SLC genes may affect how cancer cells respond to acid stress and impact on survival under the harsh chemical conditions in tumours. To link mutations with function we will identify and relate mutations with structure-function data available on transporters. With the development of new tools such as AlphaFold, it may be possible to predict the effect of mutations on transport function. Unlike many other proteins, those responsible for pH regulation can undergo a range of modifications arising from mutations, such as a change in maximal flux, affinity for substrates, cooperativity and targeting. Key predictions will be tested experimentally in appropriate cell lines holding these mutations. Where possible, we will relate the impact of mutations on patient outcomes and propose new hypotheses on how acidosis, interacting with hypoxia, influences the oncogenic process. A deliverable of this effort is a more informed approach to understanding pH regulation in cancer, driven by data from human cancers.  

Reference: 

"What can we learn about acid‑base transporters in cancer from studying somatic mutations in their genes?" White,B, Swietach, P. Pflugers Arch 2023 [in press] 

2. Curating our datasets on colorectal cancer pH related phenotypes to generate mathematical models of survival advantage under acidosis. Our lab has extensive datasets on properties relevant to pH sensing and control in a panel of 70 colorectal cancer cell lines. These include cells that are acid-sensitive and acid-resistant, produce high or low metabolic rates, and covers various permutations of mutations that might underpin these distinct phenotypes. Using principal component analysis, we were able to group cells into distinct categories and correlate these to gene expression profiles. This information must now be curated into an accessible database that can parameterise mathematical models. We will generate cell-line specific mathematical models to predict how changes in pH affect the phenotypic landscape of a tumor. Key predictions may be confirmed experimentally in co-cultures. The deliverable is a first attempt to generate a complete phenotypic resource for understanding colorectal cancer pH regulatory physiology. This will complement efforts based mainly on omics techniques such as transcriptomics.  

Reference:  

“How protons pave the way to aggressive cancers” Swietach P, Boedtkjer E, Pedersen SF. 

Nat Rev Cancer. 2023 Oct 26. doi: 10.1038/s41568-023-00628-9  

3. Understanding the correlates and the importance of a new hematological parameter, FlowScore. Recently, we showed that oxygen unloading from red blood cells is a slower process than previously anticipated. This relates to relatively slow gas diffusion across the tortuous cytoplasm packed with macromolecules. Consequently, changes in cell shape can have a profound effect on oxygen handling properties. We believe that this parameter must be considered alongside hemoglobin, a measure of storage capacity, in order to appraise the quality of blood. Thus, the oxygenation state of tissues, including tumours, will depend on how much oxygen is carried in blood (a product of flow and haemoglobin saturation) and how much oxygen can be unloaded during transit time. This becomes problematic with transfused bloods, because during storage, red cells undergo changes in metabolism and shape that favour slower unloading. The significance of this to cancer patients is that those receiving transfusions may experience suboptimal oxygen delivery to tumours, thus exacerbating their hypoxia. The factors that determine how blood “ages” in storage is unclear, but we have a surrogate, called FlowScore, that approximates the kinetic properties of red cells.  The parameters needed to measure FlowScore are recorded routinely by haematology analysers, and there are extensive datasets available to seek correlations. We have access to NIHR Bioresource data and are seeking access to WADA datasets. Our work with a consortium of blood banks provides new data. The deliverable is a better understanding of oxygen transport and its significance for tumour hypoxia.